repo.or.cz
/
gromacs.git
/
search
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
log
|
graphiclog1
|
graphiclog2
|
commit
|
commitdiff
|
tree
|
refs
|
edit
|
fork
first
·
prev
·
next
fixed PME communication range when first DD dim is not x
2010-08-03
Be
r
k Hess
f
i
xed P
M
E c
o
m
m
u
nication range when f
i
rst DD
d
im
i
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
B
e
rk Hess
m
a
de vresc
a
le and Berendsen tco
u
p
l
e
work w
i
th VV,
a
ltho
u
gh
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
B
e
rk Hess
corr
e
c
t
ed LJ on
H
of cha
r
mm tips3p
commit
|
commitdiff
|
tree
2010-07-29
Berk Hess
compl
e
t
e
d parti
a
l rename of CYN to CYS for Amber
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
corrected t
h
e A
m
ber aminoacid
s
.
r
2
b files
commit
|
commitdiff
|
tree
2010-07-28
B
e
rk Hess
r
enamed p
m
e
_
m
a
xshift0/1
t
o
pme_max
s
hift_x/y
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
replace
d
the Charmm v
s
ite parameters (which were OPLS
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Berk He
s
s
c
orrecte
d
a
vsite p
a
rame
t
er i
n
t
he amber ff's
commit
|
commitdiff
|
tree
2010-07-28
Berk Hes
s
correc
t
ed Cl atom
n
ame in amber ions
.
itp
commit
|
commitdiff
|
tree
2010-07-28
Berk He
s
s
amber
f
f ato
m
types change: corrected masses, removed
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Ber
k
Hes
s
updat
e
of amber03 aminoa
c
ids
.
rtp
,
accidentally left
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
co
r
r
ected
m
is
t
akes
i
n
amber03
g
b
sa
.
itp
commit
|
commitdiff
|
tree
2010-07-27
B
erk Hess
f
i
xed typo i
n
Makefi
l
e
commit
|
commitdiff
|
tree
2010-07-27
Ber
k
Hess
moved f
f
_dum
.
itp to the
g
mx
a
n
d gromos
ff
dire
c
t
o
ries
commit
|
commitdiff
|
tree
2010-07-27
B
e
rk Hess
corrected th
e
amber vsite paramete
r
s
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
add
e
d
h
i
s
t
o opls r
2
b
file
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
made
t
he ff fi
l
e
n
a
ming of am
b
e
r
and
c
h
armm consistent
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
B
e
rk H
e
ss
correct
e
d the am
b
er water mo
d
el files
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
fixed PME decomposition check for inverse DD order
commit
|
commitdiff
|
tree
2010-07-26
B
erk Hess
rename
d
am
b
er LYP to
L
YS and changed
names for water
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
B
erk Hess
r
emove
d
HOH from amber rna
.
hdb
commit
|
commitdiff
|
tree
2010-07-26
B
e
rk Hess
ad
d
ed missing ent
r
i
e
s for amber rna
.
hdb
commit
|
commitdiff
|
tree
2010-07-26
Berk H
e
ss
clea
n
e
d up Ambe
r
hdb's and added HO4
commit
|
commitdiff
|
tree
2010-07-26
Be
r
k Hess
re
n
amed
a
t
om types
from amber99_? et
c
.
to t
h
e o
r
iginal
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
fixed PME
c
ommun
i
cation range (no silent errors)
commit
|
commitdiff
|
tree
2010-07-26
Berk
Hess
r
e
m
oved build
i
ng block R
T
from t
h
e
lists in
s
hare/top
commit
|
commitdiff
|
tree
2010-07-26
B
erk Hess
added residue and
ato
m
renaming f
o
r AMBER
d
na
a
nd rna
commit
|
commitdiff
|
tree
2010-07-26
B
erk Hess
added DNA
a
nd RN
A
to the pdb2gmx
.
arn f
o
rmat
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
rena
m
ed O
t
o
O2 in ambe
r
rna
.
r
tp
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
added
nat
o
ms_force_co
n
str to t_forcer
e
c
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
re
n
amed
O
t
o O2 in a
m
ber dna
.
rtp
commit
|
commitdiff
|
tree
2010-07-23
Berk Hess
remove
d
garba
g
e
from checkpoint
.
c
commit
|
commitdiff
|
tree
2010-07-23
B
erk Hess
f
i
xed (rar
e
) incorrect residue
nu
m
b
e
rs whe
n
using gmx_mtop_a
.
.
.
commit
|
commitdiff
|
tree
2010-07-23
Berk Hess
added op
e
n
m
m
wr
a
ppe
r
R
F
par
a
meter checks
commit
|
commitdiff
|
tree
2010-07-19
Berk Hess
minor update to the previos ap
p
ending fix
commit
|
commitdiff
|
tree
2010-07-19
B
er
k
Hess
fixed
mdrun append ch
e
ck
when req
u
e
s
ted out
p
ut fil
e
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
Berk Hess
added m
d
p parameter f
o
r
FE
d
H tables
commit
|
commitdiff
|
tree
2010-07-05
Berk
H
ess
chang
e
d t
h
e
default
maximum
n
umber of ba
c
kup
s
fr
o
m
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
Berk H
e
s
s
removed
a lot of slow FFT
grid si
z
es fr
o
m
c
a
l
c
_
grid
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
Ber
k
Hess
documented pull co
s
ine weightin
g
commit
|
commitdiff
|
tree
2010-06-28
Berk
H
ess
re
n
amed mdrun -cptnum to
-
cpnum
commit
|
commitdiff
|
tree
2010-06-28
B
erk
H
ess
added mdrun -cptnum
o
p
t
ion to keep and
number checkpoints
commit
|
commitdiff
|
tree
2010-06-28
B
erk Hess
r
e
verted acciden
t
ial change of tabangles in g
r
ompp
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
Be
r
k
Hess
adde
d
i
n
clud
e
up
d
ate
.
h to coupling
.
c
commit
|
commitdiff
|
tree
2010-06-28
B
e
rk Hess
added back cons
t
to g
m
x_sort co
m
pare params f
o
r qsort
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Ber
k
Hess
removed
obs
o
lete fftgrid code and disabled PPPM w
i
th
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
chang
e
d pdb2g
m
x water
model ato
m
count detection
commit
|
commitdiff
|
tree
2010-06-24
Ber
k
H
e
ss
implemen
t
ed nstep
s
=-1 for mdrun continu
a
ti
o
n and tpbcon
v
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
fixed smalloc
.
h
and smalloc
.
c definition inconsistencies
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
Merge branch 'ma
s
t
er' of g
i
t@git
.
gromacs
.
org:gromac
s
commit
|
commitdiff
|
tree
2010-06-23
Berk
H
ess
removed statusio
.
h
commit
|
commitdiff
|
tree
2010-06-23
Berk Hess
fixed
g
m
x_eneconv c
o
mpiler
warnings
commit
|
commitdiff
|
tree
2010-06-23
Berk
H
ess
fixed eneconv -dt option
tempor
a
rily n
o
t writing averages
commit
|
commitdiff
|
tree
2010-06-22
Berk Hess
corrected
e
dr format
i
ssue introduced today
commit
|
commitdiff
|
tree
2010-06-21
Berk Hess
add
gmx_qsort r
o
utine,
s
i
n
ce glibc qsort is not threadsafe
.
.
.
commit
|
commitdiff
|
tree
2010-06-21
Berk Hess
fixed typo in fatal_er
r
o
r call
commit
|
commitdiff
|
tree
2010-06-18
Ber
k
Hess
now mdrun does not write the
trr file when it would
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
Berk Hess
adde
d
env var GMX_
M
A
XBACKUP
commit
|
commitdiff
|
tree
2010-06-17
Be
r
k He
s
s
fix for the previous mdrun
-
rerun c
o
mmi
t
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
mdrun
-rerun
n
ow
r
ea
d
s
t
h
e rerun traj only on t
h
e
mas
t
er
.
.
.
commit
|
commitdiff
|
tree
2010-06-17
B
erk He
s
s
m
inor update for previous re
p
l
e
x bugfix
commit
|
commitdiff
|
tree
2010-06-17
Be
r
k
Hess
fixe
d
m
dr
u
n -rerun g
i
v
i
ng NaN
with di
s
pcorr
commit
|
commitdiff
|
tree
2010-06-17
Ber
k
Hess
ad
d
ed water model s
e
lection and list file to pd
b
2gmx
commit
|
commitdiff
|
tree
2010-06-17
B
e
rk Hess
made a s
e
para
t
e tips3p
.
i
t
p f
i
le for CHARMM
commit
|
commitdiff
|
tree
2010-06-17
B
er
k
Hess
Merge br
a
nch '
m
a
s
ter' of
g
it@git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
add
e
d spce to
c
harmm27
commit
|
commitdiff
|
tree
2010-06-16
Berk
H
ess
fixed MPI crash when nat_home=0 in DD
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
rest
o
r
ed the old o
r
d
e
r of the mdru
n
opt
i
o
n
a
nd r
e
moved
.
.
.
commit
|
commitdiff
|
tree
2010-06-16
Berk Hes
s
replaced more gmx_fatal by collective c
a
ll
s
in
D
D
commit
|
commitdiff
|
tree
2010-06-16
B
e
r
k
Hess
fixed atom nam
i
ng
in enca
d
c-t
e
r
m
ini
commit
|
commitdiff
|
tree
2010-06-16
Berk
H
e
ss
with nsteps=-1 mdrun now pri
n
ts ns/day
estim
a
t
e
commit
|
commitdiff
|
tree
2010-06-16
Berk Hes
s
add
e
d
ns
t
eps=-1 option to mdp_opt
.
html
commit
|
commitdiff
|
tree
2010-06-16
B
e
rk Hess
all en
e
rgy
minimizers now do 0 steps with nsteps=0
.
.
.
commit
|
commitdiff
|
tree
2010-06-15
B
e
rk H
e
ss
fixed in
c
orrect pd
b
2gmx CYS2 to CYS renam
i
ng whi
c
h
.
.
.
commit
|
commitdiff
|
tree
2010-06-15
Berk Hess
allvsall loops
now trigger particle decomposition
commit
|
commitdiff
|
tree
2010-06-15
Berk
Hess
fatal_error in the DD
i
nitia
l
ization now calls MPI_
F
ina
l
ize
.
.
.
commit
|
commitdiff
|
tree
2010-06-14
Berk Hess
added -cwd option
t
o pdb2gmx
commit
|
commitdiff
|
tree
2010-06-11
Berk
H
ess
fixed md
r
un
c
ounter
resetting i
s
su
e
s
commit
|
commitdiff
|
tree
2010-06-11
Ber
k
Hess
optimized
the number
o
f thre
a
ds
commit
|
commitdiff
|
tree
2010-06-10
Berk Hess
m
ad
e
DD w
o
rk properly with al
l
no
n
-pe
r
iod
i
c syst
e
m
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
Berk Hess
added more explanation to idef
.
h
commit
|
commitdiff
|
tree
2010-06-10
Berk He
s
s
fi
x
ed uninitialized
variab
l
e
i
n
do_md
commit
|
commitdiff
|
tree
2010-06-10
Ber
k
H
e
s
s
fix
e
d parti
c
le deco
m
position lo
a
d print
commit
|
commitdiff
|
tree
2010-06-04
Berk Hess
fixed pdb2gmx m
e
ssing up
coor
d
inates when
d
eleting
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
Berk Hess
added no
t
es on
mdp disre parameters
commit
|
commitdiff
|
tree
2010-06-03
B
erk Hess
dist
a
n
c
e
r
estraint en
s
emble averaging is
no long
e
r
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
Berk
Hess
fixed
b
ug in enu
m
parsing error message
commit
|
commitdiff
|
tree
2010-06-03
Berk Hess
added VV pa
r
am
e
t
er
s
to md
p
_opt
.
htm
l
commit
|
commitdiff
|
tree
2010-06-02
Berk Hess
f
ixed more Gromo
s
atom t
y
pe
n
a
me ca
s
es
commit
|
commitdiff
|
tree
2010-06-01
Berk Hess
c
l
eaner f
i
x fo
r
at
o
m
type
cas
e
issue
w
ith GB parameters
commit
|
commitdiff
|
tree
2010-06-01
Ber
k
H
e
ss
fixed atom type ca
s
e issue
with GB par
a
meters
commit
|
commitdiff
|
tree
2010-06-01
B
erk
Hess
fixed two GB
bugs
commit
|
commitdiff
|
tree
2010-05-19
Be
r
k Hess
fixed mdru
n
unw
a
nti
n
gly modifying
n
st
e
nergy
a
nd n
s
tlog
commit
|
commitdiff
|
tree
2010-05-18
Berk
H
ess
i
m
plement SSE exp calcul
a
tion for s
o
l
v
e_pme
commit
|
commitdiff
|
tree
2010-05-17
B
e
rk H
e
s
s
fixed some gen
b
orn incl
u
d
e
file
d
etails
commit
|
commitdiff
|
tree
2010-05-17
Berk Hess
reordered pme_sol
v
e_yzx
a
rgume
n
ts
commit
|
commitdiff
|
tree
2010-05-14
Berk Hess
minor pme
_
sol
v
e
virial optimizat
i
on
commit
|
commitdiff
|
tree
2010-05-14
Berk Hess
fixed segv with
m
d
run -
n
pme
1
commit
|
commitdiff
|
tree
2010-05-12
Berk Hes
s
fixed cas
e
of atom type
s
in t
h
e Gromos
f
orce fields
commit
|
commitdiff
|
tree
2010-05-12
B
e
rk H
e
ss
corrected pdb2gmx f
o
r
ce field comments
commit
|
commitdiff
|
tree
next